STK: Snapshot 04-18-24 06:15 from Sierra 5.19.2-769-ge072c461

packages/stk/CHANGELOG.md

@@ -0,0 +1,5 @@
+# CHANGELOG
+
+5.19.2 (STK_VERSION 5190200) 4/17/2024
+Initial creation of STK_VERSION macro
+

packages/stk/CMakeLists.txt

@@ -34,6 +34,8 @@
 
 cmake_minimum_required(VERSION 3.16 FATAL_ERROR)
 
+message("starting STK cmake configuration, CMAKE_SOURCE_DIR=${CMAKE_SOURCE_DIR}")
+
 IF(COMMAND TRIBITS_PACKAGE_DECL)
   SET(HAVE_STK_Trilinos ON)
   TRIBITS_PACKAGE_DECL(STK)
@@ -123,6 +125,28 @@ ELSE()
   ENDIF()
 ENDIF()
 
+find_package(ArborX)
+if(TARGET ArborX::ArborX)
+  MESSAGE("found ArborX")
+  SET(STK_HAS_ARBORX ON)
+else()
+  MESSAGE("did not find ArborX. If stk_search is enabled, ArborX will not be a valid option.")
+endif()
+
+find_package(SEACAS)
+if(SEACAS_ENABLE_SEACASIoss)
+  message("found SEACASIoss")
+  SET(STK_HAS_SEACAS_IOSS ON)
+endif()
+if(SEACAS_ENABLE_SEACASExodus)
+  message("found SEACASExodus")
+  SET(STK_HAS_SEACAS_EXODUS ON)
+endif()
+if(SEACAS_ENABLE_SEACASNemesis)
+  message("found SEACASNemesis")
+  SET(STK_HAS_SEACAS_NEMESIS ON)
+endif()
+
 if(NOT HAVE_STK_Trilinos)
   stk_process_enables()
 endif()

packages/stk/cmake/Dependencies.cmake

@@ -1,26 +1,27 @@
 # the order of the packages below is important.  Stk packages can
 # depend on packages listed above them, and not below them.
 SET(SUBPACKAGES_DIRS_CLASSIFICATIONS_OPTREQS
-  Util            stk_util             PT  OPTIONAL
-  Coupling        stk_coupling         PT  OPTIONAL
-  Math            stk_math             PT  OPTIONAL
-  Simd            stk_simd             PT  OPTIONAL
-  NGP_TEST        stk_ngp_test         PT  OPTIONAL
-  ExprEval        stk_expreval         PT  OPTIONAL
-  Topology        stk_topology         PT  OPTIONAL
-  Search          stk_search           PT  OPTIONAL
-  Middle_mesh     stk_middle_mesh      EX  OPTIONAL
-  Transfer        stk_transfer         PT  OPTIONAL
-  Mesh            stk_mesh             PT  OPTIONAL
-  SearchUtil      stk_search_util      EX  OPTIONAL
-  TransferUtil    stk_transfer_util    EX  OPTIONAL
-  IO              stk_io               PT  OPTIONAL
-  Tools           stk_tools            PT  OPTIONAL
-  Balance         stk_balance          PT  OPTIONAL
-  Unit_test_utils stk_unit_test_utils  PT  OPTIONAL
-  Unit_tests      stk_unit_tests       PT  OPTIONAL
-  Doc_tests       stk_doc_tests        PT  OPTIONAL
-  Emend           stk_emend            PT  OPTIONAL
+  Util             stk_util             PT  OPTIONAL
+  Coupling         stk_coupling         PT  OPTIONAL
+  Math             stk_math             PT  OPTIONAL
+  Simd             stk_simd             PT  OPTIONAL
+  NGP_TEST         stk_ngp_test         PT  OPTIONAL
+  ExprEval         stk_expreval         PT  OPTIONAL
+  Topology         stk_topology         PT  OPTIONAL
+  Search           stk_search           PT  OPTIONAL
+  Middle_mesh      stk_middle_mesh      EX  OPTIONAL
+  Transfer         stk_transfer         PT  OPTIONAL
+  Mesh             stk_mesh             PT  OPTIONAL
+  Middle_mesh_util stk_middle_mesh_util EX  OPTIONAL
+  SearchUtil       stk_search_util      EX  OPTIONAL
+  TransferUtil     stk_transfer_util    EX  OPTIONAL
+  IO               stk_io               PT  OPTIONAL
+  Tools            stk_tools            PT  OPTIONAL
+  Balance          stk_balance          PT  OPTIONAL
+  Unit_test_utils  stk_unit_test_utils  PT  OPTIONAL
+  Unit_tests       stk_unit_tests       PT  OPTIONAL
+  Doc_tests        stk_doc_tests        PT  OPTIONAL
+  Emend            stk_emend            PT  OPTIONAL
 )
 
 SET(LIB_REQUIRED_DEP_PACKAGES)

packages/stk/cmake/STK_Trilinos_config.h.in

@@ -52,8 +52,16 @@
 
 #cmakedefine STK_HAS_MPI
 
+#cmakedefine STK_HAS_ARBORX
+
 #cmakedefine STK_VOLATILE_SIMD
 
+#cmakedefine STK_HAS_SEACAS_IOSS
+
+#cmakedefine STK_HAS_SEACAS_EXODUS
+
+#cmakedefine STK_HAS_SEACAS_NEMESIS
+
 /* Non-typical "not" macro for optional dependence on SEACASAprepro_lib (See
  * STK #17354) */
 #ifndef NOT_HAVE_STK_SEACASAPREPRO_LIB

packages/stk/cmake/stk_wrappers.cmake

@@ -75,6 +75,14 @@ function(stk_process_enables)
       set(STK_ENABLE_STKMiddle_mesh ON CACHE BOOL "")
     endif()
 
+    if (DEFINED STK_ENABLE_STKMiddle_mesh_util AND NOT STK_ENABLE_STKMiddle_mesh_util)
+      message("STKMiddle_mesh_util explicitly disabled.")
+    elseif(NOT STK_ENABLE_STKMiddle_mesh)
+      message("STKMiddle_mesh_util disabled because STKMiddle_mesh not enabled.")
+    else()
+      set(STK_ENABLE_STKMiddle_mesh_util ON CACHE BOOL "")
+    endif()
+
     if (DEFINED STK_ENABLE_STKTransfer AND NOT STK_ENABLE_STKTransfer)
       message("STKTransfer explicitly disabled.")
     elseif(NOT STK_ENABLE_STKSearch)
@@ -114,7 +122,11 @@ function(stk_process_enables)
     elseif(NOT STK_ENABLE_STKMesh)
       message("STKIO disabled because STKMesh not enabled.")
     else()
-      set(STK_ENABLE_STKIO ON CACHE BOOL "")
+      if (STK_HAS_SEACAS_IOSS)
+        set(STK_ENABLE_STKIO ON CACHE BOOL "")
+      else()
+        message("STKIO disabled because SEACASIoss not available.")
+      endif()
     endif()
 
     if (DEFINED STK_ENABLE_STKTools AND NOT STK_ENABLE_STKTools)
@@ -150,6 +162,7 @@ macro(STK_SUBPACKAGES)
 
     if(STK_ENABLE_STKCoupling)
       add_subdirectory(stk_coupling)
+      message("STKCoupling is enabled.")
     endif()
 
     if(STK_ENABLE_STKMath)
@@ -187,6 +200,11 @@ macro(STK_SUBPACKAGES)
       message("STKMiddle_mesh is enabled.")
     endif()
 
+    if(STK_ENABLE_STKMiddle_mesh_util)
+      add_subdirectory(stk_middle_mesh_util)
+      message("STKMiddle_mesh_util is enabled.")
+    endif()
+
     if(STK_ENABLE_STKTransfer)
       add_subdirectory(stk_transfer)
       message("STKTransfer is enabled.")

packages/stk/stk_balance/stk_balance/internal/NodeBalancer.cpp

@@ -122,10 +122,10 @@ NodeBalancer::exchangeLocalSizes(const std::set<int>& neighborProcessors,
   }
 
   std::vector<MPI_Status> receiveStati(receiveRequests.size());
-  MPI_Waitall(receiveRequests.size(), &receiveRequests[0], &receiveStati[0]);
+  MPI_Waitall(receiveRequests.size(), receiveRequests.data(), receiveStati.data());
 
   std::vector<MPI_Status> sendStati(sendRequests.size());
-  MPI_Waitall(sendRequests.size(), &sendRequests[0], &sendStati[0]);
+  MPI_Waitall(sendRequests.size(), sendRequests.data(), sendStati.data());
 
   int i = 0;
   for (int p : neighborProcessors) {

packages/stk/stk_balance/stk_balance/internal/StkBalanceUtils.cpp

@@ -116,7 +116,7 @@ void fillFaceBoxesWithIds(stk::mesh::BulkData &stkMeshBulkData, const BalanceSet
                                    sidesetSide, sideNodes);
       const double eps = balanceSettings.getToleranceForFaceSearch(stkMeshBulkData, *coord,
                                                                    sideNodes.data(), sideNodes.size());
-      addBoxForNodes(stkMeshBulkData, sideNodes.size(), &sideNodes[0], coord, eps,
+      addBoxForNodes(stkMeshBulkData, sideNodes.size(), sideNodes.data(), coord, eps,
           stkMeshBulkData.identifier(sidesetElement), faceBoxes);
     }
   }

packages/stk/stk_coupling/Jamfile

@@ -157,7 +157,7 @@ exe stk_coupling_utest
     [ glob $(stk_coupling-root)/../stk_unit_tests/stk_coupling/*.cpp ]
     /sierra/stk_coupling//stk_coupling
     /sierra/stk_unit_test_utils//stk_unit_main
-    /tpl/gtest//gtest
+    /tpl/googletest//gtest
 
   : <tag>@sierra-exec-tag
   ;

packages/stk/stk_doc_tests/stk_io/handleMissingFieldOnRead.cpp

@@ -38,7 +38,8 @@
 #include <iomanip>                      // for operator<<
 #include <stk_io/StkMeshIoBroker.hpp>   // for StkMeshIoBroker
 #include <stk_mesh/base/Field.hpp>      // for Field
-#include <stk_mesh/base/GetEntities.hpp>  // for get_entities
+#include <stk_mesh/base/FieldBLAS.hpp>
+#include <stk_mesh/base/ForEachEntity.hpp>
 #include <stk_mesh/base/MetaData.hpp>   // for MetaData, put_field
 #include <string>                       // for string
 #include <vector>                       // for vector
@@ -82,24 +83,17 @@ namespace {
 
       //+ The name of the field on the database will be "temp"
       stkIo.add_field(fh, temperature, "temp");
-
-      std::vector<stk::mesh::Entity> nodes;
-      stk::mesh::get_entities(stkIo.bulk_data(),
-			      stk::topology::NODE_RANK, nodes);
 
       // Add three steps to the database
       // For each step, the value of the field is the value 'time'
       for (size_t i=0; i < 3; i++) {
-	    double time = i;
+        double time = i;
 
-	    for(size_t inode=0; inode<nodes.size(); inode++) {
-        double *fieldDataForNode = stk::mesh::field_data(temperature, nodes[inode]);
-	      *fieldDataForNode = time;
-	    }
+        stk::mesh::field_fill(time, temperature);
 
-	    stkIo.begin_output_step(fh, time);
-	    stkIo.write_defined_output_fields(fh);
-	    stkIo.end_output_step(fh);
+        stkIo.begin_output_step(fh, time);
+        stkIo.write_defined_output_fields(fh);
+        stkIo.end_output_step(fh);
       }
     }
 
@@ -151,16 +145,13 @@ namespace {
       EXPECT_EQ("displacement", missing_fields[0].field()->name());
       EXPECT_EQ("disp", missing_fields[1].db_name());
       EXPECT_EQ("displacement_STKFS_N", missing_fields[1].field()->name());
-		  
+
       // The value of the "temperature" field at all nodes should be 2.0
-      std::vector<stk::mesh::Entity> nodes;
-      stk::mesh::get_entities(stkIo.bulk_data(), stk::topology::NODE_RANK,
-			      nodes);
-      for(size_t i=0; i<nodes.size(); i++) {
-        double *fieldDataForNode =
-                stk::mesh::field_data(temperature, nodes[i]);
-        EXPECT_DOUBLE_EQ(2.0, *fieldDataForNode);
-      }
+      stk::mesh::for_each_entity_run(stkIo.bulk_data(), stk::topology::NODE_RANK,
+        [&](const stk::mesh::BulkData& bulk, stk::mesh::Entity node) {
+          double *fieldDataForNode = stk::mesh::field_data(temperature, node);
+          EXPECT_DOUBLE_EQ(2.0, *fieldDataForNode);
+        });
       //-END      
     }
     // ============================================================

packages/stk/stk_doc_tests/stk_io/howToCreateAndWriteNodesetOrSideset.cpp

@@ -99,9 +99,8 @@ void verify_field_is_valid(const stk::mesh::MetaData &meta,
   stk::topology::rank_t rank = meta.mesh_bulk_data().entity_rank(entity);
   stk::mesh::FieldBase* field = meta.get_field(rank, fieldName);
   ASSERT_TRUE(field != nullptr);
-  double* fieldDataForEntity = static_cast<double*>(stk::mesh::field_data(*field, entity) );
-  unsigned numScalars = stk::mesh::field_scalars_per_entity(*field, entity);
-  ASSERT_EQ(fieldLength, numScalars);
+  const double* fieldDataForEntity = static_cast<double*>(stk::mesh::field_data(*field, entity) );
+  ASSERT_EQ(fieldLength, stk::mesh::field_scalars_per_entity(*field, entity));
   ASSERT_EQ(initialValue[0], fieldDataForEntity[0]);
 }
 

packages/stk/stk_doc_tests/stk_io/howToWriteMesh.cpp

@@ -44,14 +44,16 @@ TEST(StkIoHowTo, WriteMesh)
   unlink(filename.c_str());
 }
 
-TEST(StkIoHowTo, generateHugeMesh)
+TEST(StkIoHowTo, generateMeshWith64BitIds)
 {
   std::string meshSpec = stk::unit_test_util::simple_fields::get_option("-i", "1x1x4");
   std::string fullMeshSpec = "generated:"+meshSpec;
 
   std::string filename = "output.exo";
   stk::io::StkMeshIoBroker inputBroker;
   inputBroker.use_simple_fields();
+
+  //+ Set properties to ensure that 64-bit integers will be used
   inputBroker.property_add(Ioss::Property("INTEGER_SIZE_API" , 8));
   inputBroker.property_add(Ioss::Property("INTEGER_SIZE_DB" , 8));
   std::shared_ptr<stk::mesh::BulkData> bulk = stk::mesh::MeshBuilder(MPI_COMM_WORLD).create();

packages/stk/stk_doc_tests/stk_io/interpolateFieldCyclic.cpp

@@ -39,7 +39,8 @@
 #include <stk_io/InputFile.hpp>         // for InputFile, etc
 #include <stk_io/StkMeshIoBroker.hpp>   // for StkMeshIoBroker
 #include <stk_mesh/base/Field.hpp>      // for Field
-#include <stk_mesh/base/GetEntities.hpp>  // for get_entities
+#include <stk_mesh/base/FieldBLAS.hpp>
+#include <stk_mesh/base/ForEachEntity.hpp>
 #include <stk_mesh/base/MetaData.hpp>   // for MetaData, put_field
 #include <string>                       // for string
 #include <vector>                       // for vector
@@ -84,20 +85,12 @@ TEST(StkMeshIoBrokerHowTo, interpolateFieldCyclic)
     //+ The name of the field on the database will be "temp"
     stkIo.add_field(fh, temperature, "temp");
 
-    std::vector<stk::mesh::Entity> nodes;
-    stk::mesh::get_entities(stkIo.bulk_data(),
-                            stk::topology::NODE_RANK, nodes);
-
     // Add three steps to the database
     // For each step, the value of the field is the value 'time'
     for (size_t i=0; i < 3; i++) {
       double time = i * 10.0;
 
-      for(size_t inode=0; inode<nodes.size(); inode++) {
-        double *fieldData =
-            stk::mesh::field_data(temperature, nodes[inode]);
-        *fieldData = time;
-      }
+      stk::mesh::field_fill(time, temperature);
 
       stkIo.begin_output_step(fh, time);
       stkIo.write_defined_output_fields(fh);
@@ -138,9 +131,6 @@ TEST(StkMeshIoBrokerHowTo, interpolateFieldCyclic)
 
     stkIo.populate_bulk_data();
 
-    std::vector<stk::mesh::Entity> nodes;
-    stk::mesh::get_entities(stkIo.bulk_data(), stk::topology::NODE_RANK, nodes);
-
     // The name of the field on the database is "temp"
     stkIo.add_input_field(stk::io::MeshField(temperature, "temp",
                                              stk::io::MeshField::LINEAR_INTERPOLATION));
@@ -167,10 +157,12 @@ TEST(StkMeshIoBrokerHowTo, interpolateFieldCyclic)
       // ============================================================
       //+ VERIFICATION
       // The value of the "temperature" field at all nodes should be 'expected'
-      for(size_t i=0; i<nodes.size(); i++) {
-        double *fieldData = stk::mesh::field_data(temperature, nodes[i]);
+      stk::mesh::for_each_entity_run(stkIo.bulk_data(), stk::topology::NODE_RANK,
+        [&](const stk::mesh::BulkData& bulk, stk::mesh::Entity node) {
+        double *fieldData = stk::mesh::field_data(temperature, node);
         EXPECT_DOUBLE_EQ(expected, *fieldData);
-      }
+      });
+
       time += delta_time;
       expected += exp_inc;
       if (expected >= 20.0 || expected <= 0.0) {

packages/stk/stk_doc_tests/stk_io/interpolateFieldNegativeTime.cpp

@@ -38,7 +38,8 @@
 #include <iomanip>                      // for operator<<
 #include <stk_io/StkMeshIoBroker.hpp>   // for StkMeshIoBroker
 #include <stk_mesh/base/Field.hpp>      // for Field
-#include <stk_mesh/base/GetEntities.hpp>  // for get_entities
+#include <stk_mesh/base/FieldBLAS.hpp>
+#include <stk_mesh/base/ForEachEntity.hpp>
 #include <stk_mesh/base/MetaData.hpp>   // for MetaData, put_field
 #include <string>                       // for string
 #include <vector>                       // for vector
@@ -84,20 +85,12 @@ TEST(StkMeshIoBrokerHowTo, interpolateFieldNegativeTime)
     //+ The name of the field on the database will be "temp"
     stkIo.add_field(fh, temperature, "temp");
 
-    std::vector<stk::mesh::Entity> nodes;
-    stk::mesh::get_entities(stkIo.bulk_data(),
-                            stk::topology::NODE_RANK, nodes);
-
     // Add three steps to the database
     // For each step, the value of the field is the value 'time'
     for (int i=-2; i <= 0; i++) {
       double time = i;
 
-      for(size_t inode=0; inode<nodes.size(); inode++) {
-        double *fieldData =
-            stk::mesh::field_data(temperature, nodes[inode]);
-        *fieldData = time;
-      }
+      stk::mesh::field_fill(time, temperature);
 
       stkIo.begin_output_step(fh, time);
       stkIo.write_defined_output_fields(fh);
@@ -125,9 +118,6 @@ TEST(StkMeshIoBrokerHowTo, interpolateFieldNegativeTime)
 
     stkIo.populate_bulk_data();
 
-    std::vector<stk::mesh::Entity> nodes;
-    stk::mesh::get_entities(stkIo.bulk_data(), stk::topology::NODE_RANK, nodes);
-
     // The name of the field on the database is "temp"
     stkIo.add_input_field(stk::io::MeshField(temperature, "temp",
                                              stk::io::MeshField::LINEAR_INTERPOLATION));
@@ -141,10 +131,11 @@ TEST(StkMeshIoBrokerHowTo, interpolateFieldNegativeTime)
       // ============================================================
       //+ VERIFICATION
       // The value of the "temperature" field at all nodes should be 'time'
-      for(size_t j=0; j<nodes.size(); j++) {
-        double *fieldData = stk::mesh::field_data(temperature, nodes[j]);
-        EXPECT_DOUBLE_EQ(time, *fieldData);
-      }
+      stk::mesh::for_each_entity_run(stkIo.bulk_data(), stk::topology::NODE_RANK,
+        [&](const stk::mesh::BulkData& bulk, stk::mesh::Entity node) {
+          double *fieldData = stk::mesh::field_data(temperature, node);
+          EXPECT_DOUBLE_EQ(time, *fieldData);
+        });
     }
     //-END
   }